Agent skill

Mesh Terms Guide

by wentorai in wentorai/research-plugins

Navigate MeSH vocabulary for precise PubMed and MEDLINE searches

Install Mesh Terms Guide

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .claude/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .claude/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .agents/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .agents/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .cursor/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .cursor/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/literature/search/mesh-terms-guide

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .gemini/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .gemini/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .github/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .github/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill mesh-terms-guide -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins mesh-terms-guide --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/literature/search/mesh-terms-guide .opencode/skills/mesh-terms-guide && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "mesh-terms-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/mesh-terms-guide into .opencode/skills/mesh-terms-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mesh-terms-guide", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: mesh-terms-guide
GitHub stars: 298
Used in: 1 other repo
Token cost: ~1.3k tokens
SKILL.md length: 303 words
Files: 1
Skills in repo: 405
Repo updated: Jun 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Navigate MeSH vocabulary for precise PubMed and MEDLINE searches

Works in 5 steps: Identify 5-10 known relevant articles… → Run your MeSH search and verify all… → If any are missing, check their MeSH… → …
Tasks that involve Academic paper search
SKILL.md covers Understanding MeSH Vocabulary, Working with MeSH in PubMed, Combining MeSH with Free Text and Validating Your MeSH Strategy
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Mesh Terms Guide is an agent skill from wentorai/research-plugins. Navigate MeSH vocabulary for precise PubMed and MEDLINE searches

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Academic paper search. It works with PubMed. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

Tasks that involve Academic paper search

Example prompts

“/mesh-terms-guide”

Requirements

Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

Identify 5-10 known relevant articles (your "gold standard" set)
Run your MeSH search and verify all gold-standard articles appear
If any are missing, check their MeSH indexing to find gaps in your strategy
Scan the first 100 results to estimate precision
Adjust subheadings and explosion settings accordingly

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Mesh Terms Guide loads about 1.3k tokens when it runs. Until then it costs about 20 tokens; SKILL.md has 303 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~20
When it runs · the whole SKILL.md, loaded when a task matches: ~1.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 303 words, ~1,349 tokens.

Download SKILL.mdSave it as .claude/skills/mesh-terms-guide/SKILL.md (or your agent's skills folder).

name: mesh-terms-guide
description: Navigate MeSH vocabulary for precise PubMed and MEDLINE searches

MeSH Terms Guide

A skill for using Medical Subject Headings (MeSH) to construct precise and comprehensive biomedical literature searches. Covers MeSH tree structure, subheadings, explosion, major topics, and strategies for combining MeSH with free-text terms.

Understanding MeSH Vocabulary

What Is MeSH?

MeSH is a hierarchical controlled vocabulary maintained by the National Library of Medicine. Every article indexed in MEDLINE/PubMed is assigned MeSH terms by trained indexers. Using MeSH ensures you capture articles that discuss a concept even when authors use different terminology.

Tree Structure and Hierarchy

MeSH terms are organized in a tree with up to 13 hierarchical levels.

Example tree path for "Breast Neoplasms":

  Neoplasms [C04]
    Neoplasms by Site [C04.588]
      Breast Neoplasms [C04.588.180]
        Breast Neoplasms, Male [C04.588.180.260]
        Inflammatory Breast Neoplasms [C04.588.180.390]
        Phyllodes Tumor [C04.588.180.610]

A term can appear in multiple tree branches.
"Diabetes Mellitus, Type 2" appears under both:
  - Endocrine System Diseases
  - Metabolic Diseases

Explosion vs. Non-Explosion

# Exploded search (default in PubMed):
"Breast Neoplasms"[MeSH]
  -> Retrieves articles indexed with "Breast Neoplasms"
     AND all narrower terms underneath it

# Non-exploded search:
"Breast Neoplasms"[MeSH:NoExp]
  -> Retrieves ONLY articles indexed with "Breast Neoplasms" itself
     Does NOT include narrower terms like Inflammatory Breast Neoplasms

Working with MeSH in PubMed

Finding the Right MeSH Term

Step 1: Go to the MeSH Browser (meshb.nlm.nih.gov)
Step 2: Enter your concept (e.g., "heart attack")
Step 3: Review the mapped term: "Myocardial Infarction"
Step 4: Check Entry Terms (synonyms that map to this heading)
Step 5: Examine the tree position and scope note
Step 6: Decide whether to explode or restrict

Subheadings (Qualifiers)

MeSH subheadings refine a concept by specifying an aspect:

python

def build_mesh_query(mesh_term: str, subheadings: list[str] = None,
                     major_topic: bool = False,
                     explode: bool = True) -> str:
    """
    Build a PubMed MeSH search fragment.

    Args:
        mesh_term: The MeSH heading
        subheadings: List of MeSH subheadings (e.g., 'therapy', 'diagnosis')
        major_topic: If True, restrict to articles where this is a major topic
        explode: If False, do not include narrower terms
    """
    field = "MeSH"
    if major_topic:
        field = "Majr"

    if not explode:
        field += ":NoExp"

    if subheadings:
        sub_parts = " OR ".join(
            f'"{mesh_term}/{sh}"[{field}]' for sh in subheadings
        )
        return f"({sub_parts})"

    return f'"{mesh_term}"[{field}]'


# Example: Diabetes treatment as a major topic
print(build_mesh_query(
    "Diabetes Mellitus, Type 2",
    subheadings=["drug therapy", "therapy"],
    major_topic=True
))

Common Subheadings by Research Purpose

Purpose	Subheadings
Treatment	/therapy, /drug therapy, /surgery, /rehabilitation
Etiology	/etiology, /complications, /chemically induced
Diagnosis	/diagnosis, /diagnostic imaging, /pathology
Prevention	/prevention and control
Epidemiology	/epidemiology, /mortality, /statistics and numerical data
Genetics	/genetics, /metabolism

Combining MeSH with Free Text

Comprehensive Search Strategy

A robust search combines both MeSH terms and free-text keywords to capture all relevant articles, including those not yet indexed:

# Block 1 - MeSH terms for Concept A
("Myocardial Infarction"[MeSH] OR "Acute Coronary Syndrome"[MeSH])

# Block 2 - Free-text terms for Concept A
("myocardial infarction"[tiab] OR "heart attack"[tiab] OR
 "acute coronary"[tiab] OR "STEMI"[tiab] OR "NSTEMI"[tiab])

# Block 3 - Combine with OR
(Block 1 OR Block 2)

# Repeat for Concept B, then AND the concept blocks together

Handling Unindexed Articles

PubMed articles are often available before MeSH indexing is complete. These articles will not be found by MeSH-only searches. Always include free-text (Title/Abstract) terms alongside MeSH to capture recent publications:

"Diabetes Mellitus, Type 2"[MeSH]
OR
("type 2 diabetes"[tiab] OR "T2DM"[tiab] OR "non-insulin dependent"[tiab])

Validating Your MeSH Strategy

Recall and Precision Check

Identify 5-10 known relevant articles (your "gold standard" set)
Run your MeSH search and verify all gold-standard articles appear
If any are missing, check their MeSH indexing to find gaps in your strategy
Scan the first 100 results to estimate precision
Adjust subheadings and explosion settings accordingly

Documenting MeSH Searches for Systematic Reviews

Record the MeSH database version date, all terms used with their tree numbers, explosion status, and subheadings. This allows the search to be replicated exactly at a later date.

Files

Just SKILL.md in skills/literature/search/mesh-terms-guide of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

brycewang-stanford/Auto-Empirical-Research-Skillsskills/43-wentorai-research-plugins/skills/literature/search/mesh-terms-guide

Compare with similar skills

Mesh Terms Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Mesh Terms Guide compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Mesh Terms Guide this skillwentorai/research-plugins	298	1 repos	~1.3k	Automated safety check: Pass	MIT	3 mo ago
Literature Reviewneflibata-feng/MyArxiv-Agent	126	20 repos	~5.9k	Automated safety check: Notes	MIT	today
Citation ManagementK-Dense-AI/claude-scientific-writer	2.4k	2 repos	~3.9k	Automated safety check: Notes	MIT	today
Citation Managementneflibata-feng/MyArxiv-Agent	126	19 repos	~8.1k	Automated safety check: Notes	MIT	today
Paper Searchopenags/paper-search-mcp	2.8k	—	~1.2k	Automated safety check: Notes	MIT	7 days ago
Nature Academic Searchwp-a/nature-academic-search	301	—	~1.4k	Automated safety check: Pass	MIT	7 days ago

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Literature Review
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Questions about Mesh Terms Guide

What does Mesh Terms Guide do?

Navigate MeSH vocabulary for precise PubMed and MEDLINE searches. Mesh Terms Guide is an agent skill from wentorai/research-plugins.

When should I use Mesh Terms Guide?

Mesh Terms Guide fits situations like: tasks that involve Academic paper search.

How do I install Mesh Terms Guide in Claude Code?

Run `npx skills add wentorai/research-plugins --skill mesh-terms-guide -a claude-code`. Or copy the skill folder (skills/literature/search/mesh-terms-guide in wentorai/research-plugins) into .claude/skills/mesh-terms-guide in your project. Claude Code loads it when a task matches its description.

How do I install Mesh Terms Guide in Codex?

Run `npx skills add wentorai/research-plugins --skill mesh-terms-guide -a codex`. Or copy the skill folder (skills/literature/search/mesh-terms-guide in wentorai/research-plugins) into .agents/skills/mesh-terms-guide in your project. Codex loads it when a task matches its description.

Can I use Mesh Terms Guide in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill mesh-terms-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/mesh-terms-guide, .gemini/skills/mesh-terms-guide, .github/skills/mesh-terms-guide and .opencode/skills/mesh-terms-guide in your project.

What does Mesh Terms Guide need to run?

SKILL.md names no scripts, command-line tools or credentials: Mesh Terms Guide is instructions for the agent only. Our summary lists: Python 3.

Does Mesh Terms Guide access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Mesh Terms Guide safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Mesh Terms Guide use?

Mesh Terms Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Mesh Terms Guide use?

About 1.3k tokens (SKILL.md is roughly 5.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Mesh Terms Guide?

Skills that share tags, products or a category with Mesh Terms Guide: Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars), Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars), Citation Management (neflibata-feng/MyArxiv-Agent, 126 stars) and Paper Search (openags/paper-search-mcp, 2.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Mesh Terms Guide?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.

Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Mesh Terms Guide

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

MeSH Terms Guide

Understanding MeSH Vocabulary

What Is MeSH?

Tree Structure and Hierarchy

Explosion vs. Non-Explosion

Working with MeSH in PubMed

Finding the Right MeSH Term

Subheadings (Qualifiers)

Common Subheadings by Research Purpose

Combining MeSH with Free Text

Comprehensive Search Strategy

Handling Unindexed Articles

Validating Your MeSH Strategy

Recall and Precision Check

Documenting MeSH Searches for Systematic Reviews

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from wentorai/research-plugins

Related

Questions about Mesh Terms Guide